The ability to identify and target nucleic acid sequences that are differentially expressed and/or commonly expressed between two nucleic acid populations is of intense interest in the field of molecular biology. The identification of such differentially expressed and/or commonly expressed nucleic acid sequences can provide valuable clues as to the genetic bases for disease, inherited dominant and recessive traits, genetic alterations which give rise to diseases such as cancer, species similarities and differences, genotyping and taxonomic classification. As such, this technology has a wide range of applications in diagnostics, medicine, forensics, taxonomic classifications, and the like.
Various comparative nucleic acid techniques are available to analyze differences in nucleic acid populations. One widely known technique is referred to as "representational difference analysis" (RDA); see, for example, U.S. Pat. No. 5,436,142 and Lisitsyn, et al., Science, 259:946 (1993). RDA is a subtractive hybridization method that uses restriction digestion of genomic DNA, followed by amplification and selection methods to isolate molecules that are present in one nucleic acid population, but not in a second nucleic acid population. This method, however, requires multiple steps, numerous costly reagents and several weeks of time in the laboratory to obtain results.
Genomic analysis, particularly at the human level, is highly complex and involves the analysis of large amounts of nucleic acid. Processes which can selectively, simply and quickly isolate disease-associated sequences from complex nucleic acid samples will enable the science of molecular biology to uncover keys to the genome and, in turn, to identify the causative agents of various diseases.